Whole-genome resequencing reveals genetic differentiation and selection signatures among wild, local and commercial duck populations.

Objective: The purpose of this study was to systematically analyze the population genetic structure and genetic diversity among wild, local and commercial populations using whole-genome sequencing data from 416 individuals of 22 duck breeds in China and to further explore genetic pathways and candidate genes associated with importantly economic traits.

Methods: We performed principal component analysis, an unrooted neighbor-joining phylogenetic tree and ADMIXTURE to analyze the population structure. We compared the genetic diversity among wild, local and commercial populations using the effective population size, inbreeding coefficient, expected heterozygosity, observed heterozygosity, nucleotide diversity and regions of homozygosity. To detect selection signatures, we calculated the locus-specific branch length for local and commercial populations and calculated genetic differentiation coefficient and genetic diversity between egg and dual-purpose breeds.

Results: Wild, local and commercial duck populations formed three distinct genetic groups. The commercial population presented the lowest genetic diversity, the highest levels of inbreeding and the smallest effective population size. ADMIXTURE analysis also demonstrated that ducks were clearly divided into these three populations at K = 3. Selection signals in the commercial population were associated with growth and muscle development pathways, such as the mTOR signaling pathway and ErbB signaling pathway, and two key genomic regions (Chr1: 70.25 to 74.00 Mb and Chr2: 97.10 to 99.76 Mb) containing important genes, such as LRP6, BORCS5, and EDN1, were identified. In contrast, selection signals in the local population were associated with immune-related pathways involving NCAM2 and MPHOSPH6. Furthermore, PTGS2 and PLA2G4A genes were positively selected in egg breeds, whereas KCNK16, KCNK5, and KCNK17 genes were in dual-purpose breeds.

Conclusion: Because of artificial selection, wild, local and commercial populations presented obvious genetic differences. The selection signal analysis revealed that LRP6, BORCS5, and EDN1 are important for growth and muscle development; NCAM2 and MPHOSPH6 are for immune traits; and PTGS2 and PLA2G4A are for egg-related traits.